seqinr (version 3.1-2)

draw.oriloc: Graphical representation for nucleotide skews in prokaryotic chromosomes.

Description

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Usage

draw.oriloc(ori, main = "Title",
  xlab = "Map position in Kb",
  ylab = "Cumulated combined skew in Kb", las = 1, las.right = 3,
  ta.mtext = "Cumul. T-A skew", ta.col = "pink", ta.lwd = 1,
  cg.mtext = "Cumul. C-G skew", cg.col = "lightblue", cg.lwd = 1,
  cds.mtext = "Cumul. CDS skew", cds.col = "lightgreen", cds.lwd = 1,
  sk.col = "black", sk.lwd = 2,
  add.grid = TRUE, ...)

Arguments

ori

A data frame obtained with the oriloc function.

main

The main title of the plot.

xlab

The x-axis title.

ylab

The y-axis title.

las

The style of axis labels for the bottom and left axes.

las.right

The style of axis labels for the right axis.

ta.mtext

The marginal legend for the TA skew.

ta.col

The color for the TA skew.

ta.lwd

The line width for the TA skew.

cg.mtext

The marginal legend for the CG skew.

cg.col

The color for the CG skew.

cg.lwd

The line width for the CG skew.

cds.mtext

The marginal legend for the CDS skew.

cds.col

The color for the CDS skew.

cds.lwd

The line width for the CDS skew.

sk.col

The color for the cumulated combined skew.

sk.lwd

The line width for the cumulated combined skew.

add.grid

Logical, if TRUE a vertical grid is added to the plot.

...

Further arguments are passed to the function plot.

References

citation("seqinr")

See Also

oriloc, rearranged.oriloc, extract.breakpoints

Examples

# need internet connection
#
# Example with Chlamydia trachomatis complete genome
#
  ori <- oriloc()
  draw.oriloc(ori)
#
# The same, using more options from function draw.oriloc()
#
draw.oriloc(ori, 
  main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome),
  ta.mtext = "TA skew", ta.col = "red",
  cg.mtext = "CG skew", cg.col = "blue",
  cds.mtext = "CDS skew", cds.col = "seagreen",
  add.grid = FALSE)